H-InvDB x AHG DB
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H-Invitational ID: HIT000047666 Accession number: AK127793 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to R3H domain-containing protein 1;
 
 

Transcript original information
Accession number AK127793.1
CAGE tag ID NA
EST ID NA
Clone Number OCBBF3023913
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (R3HDM1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (R3HDM1);
Sequence data provider Project:FLJ; Provider:FLJ/HRI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 4340[bp] (No. of exon:23)[A:1314 T:1094 G:839 C:1093]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type brain
Develpmental stage fetal
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGGAG;  TAGCAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0002476
Genomic location  G-integra Help Chromosome 2
Location 2q21.3
Position 136343922- 136482838
Strand +
Possible duplicated location(s) NA
Gene structure 23 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:23518
KEGG GENES KEGG GENES(23518)
GeneCard GeneCardR3HDM1*GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS G-integraG-integra cDNA-genome alignmentcDNA-genome alignment

Predicted CDS information
HIP ID HIP000058001
Predicted CDS 230..3364;  1044[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.725

Motif information
ORF

length(1044),orf(230:3364)
MGLLLPDYRWFTTVDILADNCEKEPWIILFYFCGTPQSQIQRTHQEKIQI
QLTQSFEKEEKPSKDEAEKEKASDKLPRKMLSRDSSQEYTDSTGIDLHEF
LVNTLKNNPRDRMMLLKLEQEILDFIGNNESPRKKFPPMTSYHRMLLHRV
AAYFGLDHNVDQSGKSVIVNKTSNTRIPDQKFNEHIKDDKGEDFQKRYIL
KRDNSSFDKDDNQMRIRLKDDRRSKSIEEREEEYQRARDRIFSQDSLCSQ
ENYIIDKRLQDEDASSTQQRRQIFRVNKDASGRSTNSHQSSTENELKYSE
PRPWSSTDSDSSLRNLKPAVTKASSFSGISVLTRGDSSGSSKSIGRLSKT
GSESSGSVGSSTGSLSHIQQPLPGTALSQSSHGAPVVYPTVSTHSSLSFD
GGLNGQVASPSTSFFLLPLEAAGIPPGSILINPQTGQPFINPDGSPVVYN
PPMTQQPVRSQVPGPPQPPLPAPPQQPAANHIFSQQDNLGSQFSHMSLAR
QPSADGSDPHAAMFQSTVVLQSPQQSGYIMTAAPPPHPPPPPPPPPPPPP
LPPGQPVPTAGYPASGHPVSQPVLQQPGYIQQPSPQMPACYCAPGHYHSS
QPQYRPVPSVHYNSHLNQPLPQPAQQTGYQVIPNQQQNYQGIVGVQQPQS
QSLVSGQPNSIGNQIQGVVIPYTSVPTYQVSLPQGSQGIPHQTYQQPVMF
PNQSNQGSMPTTGMPVYYSVIPPGQQNNLSSSVGYLQHPGSEQVQFPRTT
SPCSSQQLQGHQCTAGPPPPPGGGMVMMQLSVPNNPQSCAHSPPQWKQNK
YYCDHQRGQKCVEFSSVDNIVQHSPQLSSPIISPAQSPAPAQLSTLKTVR
PSGPPLSIMPQFSRPFVPGQGDSRYPLLGQPLQYNPPAVLHGHIPNQQGQ
PGSRHGNRGRRQAKKAASTDLGAGETVVGKVLEITELPDGITRMEAEKLF
GELFKIGAKIRWLRDPQSQPRRHPLCCGSGDNTANPERSKPSDLASTYTV
...
a.a.
length
InterPro Name
length(122), motif(84:205) 122 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(78), motif(95:172) 78 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(64), motif(112:175) 64 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(61), motif(112:172) 61 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(64), motif(115:178) 64 IPR001374 Single-stranded nucleic acid binding R3H [Domain]
length(71), motif(176:246) 71 IPR024771 SUZ domain [Domain]
length(51), motif(195:245) 51 IPR024771 SUZ domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000047666
H-Inv cluster ID Locus viewHIX0002476
Accession number AK127793.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Similar to R3H domain-containing protein 1;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q15032)  [Identity/coverage = 99.107%/91.72%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 7584026151441861548933418669648196903322006823121406692ALL
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol R3HDM1
HGNC aliases "R3H domain (binds single-stranded nucleic acids) containing"
HGNC name R3H domain containing 1
DDBJ NA
UniProt R3HDM1
EC number NA
GGDB
(GlycoGene Database)
Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000058001
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:23518
KEGG GENES KEGG GENES(23518)
GeneCard GeneCardR3HDM1*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Auto-annotated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool;  TACTTACT
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA

Gene ontology information
Molecular function nucleic acid binding (GO:0003676); 

Subcellular localization information  Last modified:27-May-2015
WoLF PSORT nuclear;  cytosol; 
Target P Other
SOSUI soluble protein
TMHMM soluble protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
85 205 1whrA 9e-33 75.2 121/124 d.68.7.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene AGhsA240320; 
Affymetrix
GeneChip
HG-Focus NA
HG-U133 202754_at; 
HG-U133A 202754_at; 
HG-U133A_2 202754_at; 
HG-U133B NA
HG-U133_Plus_2 202754_at; 
HG-U95 36610_at; 
HG-U95A 36610_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2507395;  2507396;  2507402;  2507415;  2507416;  2507420;  2507421;  2507422;  2507425;  2507427;  2507429;  2507430;  2507431;  2507432;  2507435;  2507437;  2507438;  2507443;  2507444;  2507445;  2507448;  2507449;  2507460;  2507461;  2507471;  2507472;  2507475;  2507476;  2507480;  2507481;  2507482;  2507483;  2577840;  2577848; 
HuGeneFL D21852_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P380998; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P380998; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
54 .. 54 G/C rs140937367 + 5'UTR
406 .. 406 A/C rs150951840 + CDS Nonsynonymous[Glu59Asp]
437 .. 437 G/A rs143615820 + CDS Nonsynonymous[Glu70Lys]
489 .. 489 A/C rs201209663 + CDS Nonsynonymous[Gln87Pro]
627 .. 627 G/A rs144742726 + CDS Nonsynonymous[Arg133His]
869 .. 869 A/G rs961360 - CDS Nonsynonymous[Met214Val]
980 .. 980 G/A rs202129033 + CDS Nonsynonymous[Glu251Lys]
989 .. 989 A/C rs34088964 - CDS Nonsynonymous[Ile254Leu]
1010 .. 1010 G/A rs139991249 + CDS Nonsynonymous[Asp261Asn]
1041 .. 1041 G/A rs202036518 + CDS Nonsynonymous[Arg271His]
1104 .. 1104 C/G rs114219457 + CDS Nonsynonymous[Thr292Ser]
1191 .. 1191 C/T rs182409818 + CDS Nonsynonymous[Thr321Ile]
1328 .. 1328 C/T rs199860629 + CDS Nonsynonymous[His367Tyr]
1451 .. 1451 G/A rs140932904 + CDS Nonsynonymous[Ala408Thr]
1491 .. 1491 C/G rs147536237 + CDS Nonsynonymous[Ala421Gly]
1492 .. 1492 G/A rs149874194 + CDS Synonymous[Ala421Ala]
1495 .. 1495 A/C rs144901752 + CDS Synonymous[Ala422Ala]
1496 .. 1496 G/C rs143277081 + CDS Nonsynonymous[Gly423Arg]
1530 .. 1530 A/G rs116803765 + CDS Nonsynonymous[Gln434Arg]
1533 .. 1533 C/T rs140890871 + CDS Nonsynonymous[Thr435Ile]
1590 .. 1590 C/T rs150394823 + CDS Nonsynonymous[Thr454Ile]
1648 .. 1648 A/T rs13425947 + CDS Synonymous[Pro473Pro]
1702 .. 1702 T/C rs139193845 + CDS Synonymous[Ser491Ser]
1762 .. 1762 C/T rs147519491 + CDS Synonymous[Ala511Ala]
1806 .. 1806 C/G rs201789029 + CDS Nonsynonymous[Ser526Cys]
1829 .. 1829 C/A rs112729561 + CDS Nonsynonymous[Pro534Thr]
1831 .. 1831 T/C rs201061461 + CDS Synonymous[Pro534Pro]
1839 .. 1839 A/G rs150498555 + CDS Nonsynonymous[His537Arg]
1843 .. 1843 T/C rs200431099 + CDS Synonymous[Pro538Pro]
1866 .. 1866 C/T rs139457585 + CDS Nonsynonymous[Pro546Leu]
1876 .. 1876 T/C rs111235534 + CDS Synonymous[Pro549Pro]
1927 .. 1927 T/A rs202173447 + CDS Synonymous[Gly566Gly]
1959 .. 1959 C/A rs2305165 - CDS Nonsynonymous[Pro577Gln]
2006 .. 2006 G/A rs144077610 + CDS Nonsynonymous[Ala593Thr]
2016 .. 2016 A/G rs139502420 + CDS Nonsynonymous[His596Arg]
2042 .. 2042 C/T rs114677169 + CDS Nonsynonymous[Arg605Cys]
2046 .. 2046 C/T rs151233134 + CDS Nonsynonymous[Pro606Leu]
2100 .. 2100 C/T rs199515262 + CDS Nonsynonymous[Ala624Val]
2101 .. 2101 G/A rs139125340 + CDS Synonymous[Ala624Ala]
2157 .. 2157 T/G rs201906607 + CDS Nonsynonymous[Val643Gly]
2182 .. 2182 G/C rs143127486 + CDS Nonsynonymous[Gln651His]
2188 .. 2188 A/G rs149624809 + CDS Synonymous[Leu653Leu]
2281 .. 2281 A/G rs144388261 + CDS Synonymous[Gln684Gln]
2357 .. 2357 C/A rs76298784 + CDS Nonsynonymous[Pro710Thr]
2422 .. 2422 T/C rs199864603 + CDS Synonymous[Ser731Ser]
2475 .. 2475 C/T rs200294484 + CDS Nonsynonymous[Thr749Ile]
2508 .. 2508 G/A rs199587789 + CDS Nonsynonymous[Gly760Asp]
2522 .. 2522 G/A rs144042865 + CDS Nonsynonymous[Ala765Thr]
2531 .. 2531 C/A rs139565775 + CDS Nonsynonymous[Pro768Thr]
2610 .. 2610 C/T rs145608320 + CDS Nonsynonymous[Pro794Leu]
2611 .. 2611 G/A rs147882808 + CDS Synonymous[Pro794Pro]
2642 .. 2642 C/T rs143703596 + CDS Nonsynonymous[His805Tyr]
2647 .. 2647 G/A rs200624357 + CDS Synonymous[Gln806Gln]
2685 .. 2685 A/G rs148125749 + CDS Nonsynonymous[Asn819Ser]
2716 .. 2716 C/G rs115242070 + CDS Nonsynonymous[Ser829Arg]
2729 .. 2729 C/T rs201494950 + CDS Nonsynonymous[Pro834Ser]
2834 .. 2834 G/A rs116821936 + CDS Nonsynonymous[Gly869Arg]
2884 .. 2884 T/C rs199595729 + CDS Synonymous[Asn885Asn]
2902 .. 2902 C/T rs35003255 - CDS Synonymous[His891His]
2997 .. 2997 C/T rs115519111 + CDS Nonsynonymous[Ala923Val]
3018 .. 3018 A/T rs199512616 + CDS Nonsynonymous[Lys930Met]
3043 .. 3043 A/G rs113498203 + CDS Synonymous[Pro938Pro]
3144 .. 3144 G/A rs143951307 + CDS Nonsynonymous[Arg972His]
3147 .. 3147 A/G rs148646134 + CDS Nonsynonymous[His973Arg]
3166 .. 3166 T/G rs200059770 + CDS Nonsynonymous[Ser979Arg]
3171 .. 3171 A/G rs72844194 + CDS Nonsynonymous[Asp981Gly]
3185 .. 3185 C/A rs116105123 + CDS Nonsynonymous[Pro986Thr]
3192 .. 3192 G/A rs114639828 + CDS Nonsynonymous[Arg988His]
3283 .. 3283 T/G rs147866381 + CDS Nonsynonymous[Ile1018Met]
3287 .. 3287 T/G rs190617868 + CDS Nonsynonymous[Ser1020Ala]
3321 .. 3321 A/G rs141539490 + CDS Nonsynonymous[Lys1031Arg]
3322 .. 3322 G/A rs145238803 + CDS Synonymous[Lys1031Lys]
3363 .. 3363 A/G rs116499913 + CDS Synonymous_atSTOP[*1045*]
3381 .. 3381 C/T rs182869080 + 3'UTR
3382 .. 3382 T/A rs78511053 + 3'UTR
3470 .. 3470 T/C rs187633452 + 3'UTR
3562 .. 3562 A/G rs116610856 + 3'UTR
3682 .. 3682 T/C rs3739027 - 3'UTR
3722 ^ 3723 -/C rs57955497 + 3'UTR
3747 .. 3747 A/C rs191985045 + 3'UTR
3821 .. 3821 T/G rs143064512 + 3'UTR
4060 .. 4060 T/- rs71672054 + 3'UTR
4076 .. 4076 A/C rs75006798 + 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD)
Related H-InvDB links VaryGeneVaryGene Repeat mask viewerRepeat Mask Viewer